Pathway Studio

Category Cross-Omics>Pathway Analysis/Tools

Abstract Pathway Studio is a pathway analysis suite of interactive software for building and displaying the relationships between biological molecules and processes. Product includes Medscan (see G6G Abstract Number 20090) and pathways databases. Pathway Studio is available in two (2) editions tailored to suit your research needs. Pathway Studio Desktop delivers all the tools needed to support basic research by individuals or work groups and includes the advanced MedScan technology for extending the ResNet database (see G6G Abstract Number 20021). Pathway Studio Enterprise includes advanced capability with support for large installations and for advanced personal research.

Pathway Studio features includes:

Desktop software - 1) Build and visualize pathways; 2) Analyze and curate pathways; 3) Import and analyze gene & protein lists; 4) Interpret microarray gene expression data; 5) Analyze proteomics and metabolomics data.

MedScan Technology - 1) Search and mine the literature; 2) Extract interactions from the literature; 3) Build targeted data content.

Database Management system - 1) ResNet database; 2) Interrogate different species, multiple genomes; 3) Supports public and commercial databases.

Product offers a Web Client and a PC Client for the Pathway Studio Enterprise edition.

Pathway Visualization - 1) Graphical user interface for drawing, coloring, viewing, editing and annotation of pathway and relationship maps; 2) Automatic layout algorithms revealing pathway organization; 3) Publication-quality illustrations in all major image file formats; 4) Export of pathways as clickable HTML or XML files.

Pathway Analysis and Curation - 1) Create your own pathways and produce publication quality graphics and diagrams; 2) Optimize views by filtering, pathway expansion, and protein classification; 3) Build pathways for gene lists imported from microarray and other experiments; 4) Display specific upstream and downstream events; 5) Find interaction paths among molecules, cell objects and processes; 6) Determine and identify common targets and regulators for a group of proteins.

Molecular Interaction Networks from the Literature - 1) Analyze pathways with ResNet database, compiled from PubMed abstracts and articles; 2) Access more than 1,000,000 facts of regulation, interaction and modification; 3) Validate the facts by clicking on the link to an original sentence, abstract or source.

Pathway Reconstruction Algorithms - 1) "Build Pathway" is an advanced search tool with flexible options to navigate the network database and build pathways. Choose from multiple algorithms for assembling a pathway such as "find only direct interactions", "find shortest paths", "find common targets" or "find common regulators"; 2) "Find relevant networks" - finds pathways related to a list of molecules; 3) Find differentially expressed networks (pathways) for a microarray experiment.

Data Mining and Searches - 1) Find all interacting molecules for a protein or other biological entity; 2) Find all networks/pathways for a query protein; 3) Use context and field-specific database searches; 4) Filter to see only specific types of biological objects to be included in your pathway, such as proteins, complexes, small molecules, cellular processes etc; 5) Filter to see only specific types of biological interactions such as binding interactions, post-translational regulation, expression regulation, enzymatic activity, molecular synthesis, transport, and others; 6) Review original literature sources for every relation within a pathway via direct links to PubMed abstract and exact source sentence where each finding is referenced.

Import and Analysis of Gene & Protein Lists - 1) Import/export gene and protein lists; 2) Map gene lists on signaling and metabolic pathways, and GO groups; 3) Build and analyze pathways from imported lists; 4) Work with protein IDs, names or aliases from various sources - Unigene IDs, Accession Numbers, LocusLink, Swiss-Prot, Affymetrix GeneChip IDs, Gene Names and Gene Symbols.

Literature Mining - 1) Use integrated MedScan software to extract biological interactions from scientific text; 2) Mine PubMed and build pathways from extracted facts; 3) Update pathways using data from recent publications.

Microarray Gene Expression Data Analysis - 1) Import data from all popular microarray analysis software packages; 2) Reconstruct molecular networks from gene expression and proteomics data; 3) View how genes in a pathway are up or down regulated through various biological states to identify key regulators or targets of interest.

Dynamic Modeling - PathwaySolver pathway dynamics analysis module of Pathway Studio emulates the dynamics of biological pathways by calculating concentrations of proteins and biochemical compounds during time course and treatment experiments and conditions - PathwaySolver can help you - 1) Predict the effects of knockouts of various biological entities; 2) Optimize the product release in metabolic pathways; 3) Assess system stability in relationship to changes in parameters.

Supported Data Formats - 1) ResNet Exchange (RNEF) XML and SBML formats for molecular network data; 2) Simple tab-delimited format for molecular interaction data import from KEGG, BIND, DIP, STKE, GO and other leading pathway databases; 3) Flexible tab-delimited format for microarray data import; 4) Multiple microarray platforms including Affymetrix, Agilent, etc; 5) Both raw and pre-processed microarray data. And more.

Note: Ariadne information extraction, data management and pathway analysis products incorporate unique proprietary technologies - A set of state-of-the-art Natural Language Processing (NLP) and data mining algorithms that are applied in a coherent fashion to automatically extract data from literature. The result is databases of genomics & proteomics knowledge represented in a formalized structure with the focus on how the proteins, cell processes and small molecules interact, modify and regulate each other (pathways).

System Requirements

Pathway Studio Desktop

Pathway Studio Workgroup

Workgroup PC Client

Workgroup Server

Pathway Studio Enterprise

Enterprise PC Client

Enterprise Server


Manufacturer Web Site Ariadne Genomics, Inc.

Price Contact manufacturer.

G6G Abstract Number 20020

G6G Manufacturer Number 100335